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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 596 by gezelter, Mon Jul 14 15:04:55 2003 UTC vs.
Revision 843 by mmeineke, Wed Oct 29 20:41:39 2003 UTC

# Line 1 | Line 1
1   #ifndef _INTEGRATOR_H_
2   #define _INTEGRATOR_H_
3  
4 + #include <string>
5 + #include <vector>
6   #include "Atom.hpp"
7 + #include "Molecule.hpp"
8   #include "SRI.hpp"
9   #include "AbstractClasses.hpp"
10   #include "SimInfo.hpp"
11   #include "ForceFields.hpp"
12   #include "Thermo.hpp"
13   #include "ReadWrite.hpp"
14 + #include "ZConsWriter.hpp"
15  
16 + using namespace std;
17   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
18   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19   const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
20   const int maxIteration = 300;
21   const double tol = 1.0e-6;
22  
18 – class Integrator : public BaseIntegrator {
23  
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31 +  virtual string getAdditionalParameters(void);
32  
25 –
33   protected:
34 <  
34 >
35    virtual void integrateStep( int calcPot, int calcStress );
36    virtual void preMove( void );
37    virtual void moveA( void );
# Line 32 | Line 39 | class Integrator : public BaseIntegrator { (protected)
39    virtual void constrainA( void );
40    virtual void constrainB( void );
41    virtual int  readyCheck( void ) { return 1; }
35 –  
36 –  void checkConstraints( void );
37 –  void rotate( int axes1, int axes2, double angle, double j[3],
38 –               double A[3][3] );
42  
43 +  virtual void resetIntegrator( void ) { }
44  
45 +  virtual void calcForce( int calcPot, int calcStress );
46 +  virtual void thermalize();
47 +
48 +  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
49 +
50 +  void checkConstraints( void );
51 +  void rotate( int axes1, int axes2, double angle, double j[3],
52 +         double A[3][3] );
53 +
54    ForceFields* myFF;
55  
56    SimInfo *info; // all the info we'll ever need
# Line 48 | Line 61 | class Integrator : public BaseIntegrator { (protected)
61    int nMols;
62  
63    int isConstrained; // boolean to know whether the systems contains
64 <                     // constraints.
65 <  int nConstrained;  // counter for number of constraints
66 <  int *constrainedA; // the i of a constraint pair
67 <  int *constrainedB; // the j of a constraint pair
68 <  double *constrainedDsqr; // the square of the constraint distance
69 <  
64 >         // constraints.
65 >  int nConstrained;  // counter for number of constraints
66 >  int *constrainedA; // the i of a constraint pair
67 >  int *constrainedB; // the j of a constraint pair
68 >  double *constrainedDsqr; // the square of the constraint distance
69 >
70    int* moving; // tells whether we are moving atom i
71    int* moved;  // tells whether we have moved atom i
72 <  double* oldPos; // pre constrained positions
72 >  double* oldPos; // pre constrained positions
73  
74    short isFirst; /*boolean for the first time integrate is called */
75 <  
75 >
76    double dt;
77    double dt2;
78  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –
79    Thermo *tStats;
80    StatWriter*  statOut;
81    DumpWriter*  dumpOut;
82 <  
82 >
83   };
84  
85 < class NVE : public Integrator{
85 > typedef Integrator<BaseIntegrator> RealIntegrator;
86  
87 + template<typename T> class NVE : public T {
88 +
89   public:
90    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
91 <    Integrator( theInfo, the_ff ){}
91 >    T( theInfo, the_ff ){}
92    virtual ~NVE(){}
84 –
85 –  
86 –
93   };
94  
89 – class NVT : public Integrator{
95  
96 + template<typename T> class NVT : public T {
97 +
98   public:
99  
100    NVT ( SimInfo *theInfo, ForceFields* the_ff);
101 <  virtual ~NVT() {}
101 >  virtual ~NVT();
102  
103    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
104    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
105 +  void setChiTolerance(double tol) {chiTolerance = tol;}
106 +  virtual double  getConservedQuantity(void);
107 +  virtual string getAdditionalParameters(void);
108  
109   protected:
110  
# Line 103 | Line 113 | class NVT : public Integrator{ (protected)
113  
114    virtual int readyCheck();
115  
116 +  virtual void resetIntegrator( void );
117 +
118    // chi is a propagated degree of freedom.
119  
120    double chi;
121  
122 +  //integral of chi(t)dt
123 +  double integralOfChidt;
124 +
125    // targetTemp must be set.  tauThermostat must also be set;
126  
127    double targetTemp;
128    double tauThermostat;
129 <  
129 >
130    short int have_tau_thermostat, have_target_temp;
131  
132 +  double *oldVel;
133 +  double *oldJi;
134 +
135 +  double chiTolerance;
136 +  short int have_chi_tolerance;
137 +
138   };
139  
140  
120 – class NPTi : public Integrator{
141  
142 + template<typename T> class NPT : public T{
143 +
144   public:
145  
146 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
147 <  virtual ~NPTi() {};
146 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
147 >  virtual ~NPT();
148  
149    virtual void integrateStep( int calcPot, int calcStress ){
150      calcStress = 1;
151 <    Integrator::integrateStep( calcPot, calcStress );
151 >    T::integrateStep( calcPot, calcStress );
152    }
153  
154 +  virtual double getConservedQuantity(void) = 0;
155 +  virtual string getAdditionalParameters(void) = 0;
156 +  
157 +  double myTauThermo( void ) { return tauThermostat; }
158 +  double myTauBaro( void ) { return tauBarostat; }
159 +
160    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
161    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
162    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
163    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
164 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
165 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
166 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
167  
168   protected:
169  
# Line 141 | Line 172 | class NPTi : public Integrator{ (protected)
172  
173    virtual int readyCheck();
174  
175 <  // chi and eta are the propagated degrees of freedom
175 >  virtual void resetIntegrator( void );
176  
177 <  double chi;
178 <  double eta;
179 <  double NkBT;
177 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
178 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
179 >  virtual void getPosScale(double pos[3], double COM[3],
180 >                           int index, double sc[3]) = 0;
181  
182 <  // targetTemp, targetPressure, and tauBarostat must be set.  
183 <  // One of qmass or tauThermostat must be set;
182 >  virtual bool chiConverged( void );
183 >  virtual bool etaConverged( void ) = 0;
184  
185 <  double targetTemp;
186 <  double targetPressure;
187 <  double tauThermostat;
188 <  double tauBarostat;
157 <
158 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
159 <  short int have_target_pressure;
185 >  virtual void evolveChiA( void );
186 >  virtual void evolveEtaA( void ) = 0;
187 >  virtual void evolveChiB( void );
188 >  virtual void evolveEtaB( void ) = 0;
189  
190 < };
190 >  virtual void scaleSimBox( void ) = 0;
191  
192 < class NPTim : public Integrator{
192 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
193  
165 – public:
166 –
167 –  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
168 –  virtual ~NPTim() {};
169 –
170 –  virtual void integrateStep( int calcPot, int calcStress ){
171 –    calcStress = 1;
172 –    Integrator::integrateStep( calcPot, calcStress );
173 –  }
174 –
175 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
176 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
177 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
178 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
179 –
180 – protected:
181 –
182 –  virtual void  moveA( void );
183 –  virtual void moveB( void );
184 –
185 –  virtual int readyCheck();
186 –
194    // chi and eta are the propagated degrees of freedom
195  
196 +  double oldChi;
197 +  double prevChi;
198    double chi;
190 –  double eta;
199    double NkBT;
200 +  double fkBT;
201  
202 <  // targetTemp, targetPressure, and tauBarostat must be set.  
202 >  double tt2, tb2;
203 >  double instaTemp, instaPress, instaVol;
204 >  double press[3][3];
205 >
206 >  int Nparticles;
207 >
208 >  double integralOfChidt;
209 >
210 >  // targetTemp, targetPressure, and tauBarostat must be set.
211    // One of qmass or tauThermostat must be set;
212  
213    double targetTemp;
# Line 201 | Line 218 | class NPTim : public Integrator{ (protected)
218    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
219    short int have_target_pressure;
220  
221 +  double *oldPos;
222 +  double *oldVel;
223 +  double *oldJi;
224 +
225 +  double chiTolerance;
226 +  short int have_chi_tolerance;
227 +  double posIterTolerance;
228 +  short int have_pos_iter_tolerance;
229 +  double etaTolerance;
230 +  short int have_eta_tolerance;
231 +
232   };
233  
234 < class NPTf : public Integrator{
234 > template<typename T> class NPTi : public T{
235  
236   public:
237 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
238 +  ~NPTi();
239  
240 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
241 <  virtual ~NPTf() {};
240 >  virtual double getConservedQuantity(void);
241 >  virtual void resetIntegrator(void);
242 >  virtual string getAdditionalParameters(void);
243 > protected:
244  
213 –  virtual void integrateStep( int calcPot, int calcStress ){
214 –    calcStress = 1;
215 –    Integrator::integrateStep( calcPot, calcStress );
216 –  }
245  
218 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
219 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
220 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
221 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
246  
247 +  virtual void evolveEtaA(void);
248 +  virtual void evolveEtaB(void);
249 +
250 +  virtual bool etaConverged( void );
251 +
252 +  virtual void scaleSimBox( void );
253 +
254 +  virtual void getVelScaleA( double sc[3], double vel[3] );
255 +  virtual void getVelScaleB( double sc[3], int index );
256 +  virtual void getPosScale(double pos[3], double COM[3],
257 +                           int index, double sc[3]);
258 +
259 +  double eta, oldEta, prevEta;
260 + };
261 +
262 + template<typename T> class NPTf : public T{
263 +
264 + public:
265 +
266 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
267 +  virtual ~NPTf();
268 +
269 +  virtual double getConservedQuantity(void);
270 +  virtual string getAdditionalParameters(void);
271 +  virtual void resetIntegrator(void);
272 +
273   protected:
274  
275 <  virtual void  moveA( void );
276 <  virtual void moveB( void );
275 >  virtual void evolveEtaA(void);
276 >  virtual void evolveEtaB(void);
277  
278 <  virtual int readyCheck();
278 >  virtual bool etaConverged( void );
279  
280 <  // chi and eta are the propagated degrees of freedom
280 >  virtual void scaleSimBox( void );
281  
282 <  double chi;
283 <  double eta[3][3];
284 <  double NkBT;
282 >  virtual void getVelScaleA( double sc[3], double vel[3] );
283 >  virtual void getVelScaleB( double sc[3], int index );
284 >  virtual void getPosScale(double pos[3], double COM[3],
285 >                           int index, double sc[3]);
286  
287 <  // targetTemp, targetPressure, and tauBarostat must be set.  
288 <  // One of qmass or tauThermostat must be set;
287 >  double eta[3][3];
288 >  double oldEta[3][3];
289 >  double prevEta[3][3];
290 > };
291  
292 <  double targetTemp;
240 <  double targetPressure;
241 <  double tauThermostat;
242 <  double tauBarostat;
292 > template<typename T> class NPTxyz : public T{
293  
294 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
245 <  short int have_target_pressure;
294 > public:
295  
296 +  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
297 +  virtual ~NPTxyz();
298 +
299 +  virtual double getConservedQuantity(void);
300 +  virtual string getAdditionalParameters(void);
301 +  virtual void resetIntegrator(void);
302 +
303 + protected:
304 +
305 +  virtual void evolveEtaA(void);
306 +  virtual void evolveEtaB(void);
307 +
308 +  virtual bool etaConverged( void );
309 +
310 +  virtual void scaleSimBox( void );
311 +
312 +  virtual void getVelScaleA( double sc[3], double vel[3] );
313 +  virtual void getVelScaleB( double sc[3], int index );
314 +  virtual void getPosScale(double pos[3], double COM[3],
315 +                           int index, double sc[3]);
316 +
317 +  double eta[3][3];
318 +  double oldEta[3][3];
319 +  double prevEta[3][3];
320   };
321  
249 – class NPTfm : public Integrator{
322  
323 + template<typename T> class ZConstraint : public T {
324 +
325 +  public:
326 +  class ForceSubtractionPolicy{
327 +    public:
328 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
329 +
330 +      virtual void update() = 0;
331 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
332 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
333 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
334 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
335 +
336 +   protected:
337 +     ZConstraint<T>* zconsIntegrator;
338 +  };
339 +
340 +  class PolicyByNumber : public ForceSubtractionPolicy{
341 +
342 +    public:
343 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
344 +      virtual void update();
345 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
346 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
347 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
348 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
349 +
350 +    private:
351 +      int totNumOfMovingAtoms;
352 +  };
353 +
354 +  class PolicyByMass : public ForceSubtractionPolicy{
355 +
356 +    public:
357 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 +
359 +      virtual void update();
360 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
361 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
362 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
363 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
364 +
365 +   private:
366 +     double totMassOfMovingAtoms;
367 +  };
368 +
369   public:
370  
371 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
372 <  virtual ~NPTfm() {};
371 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
372 >  ~ZConstraint();
373  
374 <  virtual void integrateStep( int calcPot, int calcStress ){
375 <    calcStress = 1;
258 <    Integrator::integrateStep( calcPot, calcStress );
259 <  }
374 >  void setZConsTime(double time)                  {this->zconsTime = time;}
375 >  void getZConsTime()                             {return zconsTime;}
376  
377 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
378 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
263 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
264 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
377 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
378 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
379  
380 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
381 +  string getZConsOutput()                         {return zconsOutput;}
382 +
383 +  virtual void integrate();
384 +
385 +
386 + #ifdef IS_MPI
387 +  virtual void update();                      //which is called to indicate the molecules' migration
388 + #endif
389 +
390 +  enum ZConsState {zcsMoving, zcsFixed};
391 +
392 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
393 +  vector<ZConsState> states;                 //state of z-constraint molecules
394 +
395 +
396 +
397 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
398 +  double totalMassOfUncons;                //total mas of unconstraint molecules
399 +
400 +
401   protected:
402  
268 –  virtual void  moveA( void );
269 –  virtual void moveB( void );
403  
271 –  virtual int readyCheck();
404  
405 <  // chi and eta are the propagated degrees of freedom
405 >  virtual void calcForce( int calcPot, int calcStress );
406 >  virtual void thermalize(void);
407  
408 <  double chi;
409 <  double eta[3][3];
410 <  double NkBT;
408 >  void zeroOutVel();
409 >  void doZconstraintForce();
410 >  void doHarmonic();
411 >  bool checkZConsState();
412  
413 <  // targetTemp, targetPressure, and tauBarostat must be set.  
414 <  // One of qmass or tauThermostat must be set;
413 >  bool haveFixedZMols();
414 >  bool haveMovingZMols();
415  
416 <  double targetTemp;
283 <  double targetPressure;
284 <  double tauThermostat;
285 <  double tauBarostat;
416 >  double calcZSys();
417  
418 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
288 <  short int have_target_pressure;
418 >  int isZConstraintMol(Molecule* mol);
419  
420 +
421 +  double zconsTime;                              //sample time
422 +  double zconsTol;                                 //tolerance of z-contratint
423 +  double zForceConst;                           //base force constant term
424 +                                                          //which is estimate by OOPSE
425 +
426 +
427 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
428 +  vector<double> kz;                              //force constant array
429 +
430 +  vector<double> zPos;                          //
431 +
432 +
433 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
434 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
435 +
436 +
437 +  vector<ZConsParaItem>* parameters; //
438 +
439 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
440 +
441 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
442 +  double* fz;
443 +  double* curZPos;
444 +
445 +
446 +
447 +  int whichDirection;                           //constraint direction
448 +
449 + private:
450 +
451 +  string zconsOutput;                         //filename of zconstraint output
452 +  ZConsWriter* fzOut;                         //z-constraint writer
453 +
454 +  double curZconsTime;
455 +
456 +  double calcMovingMolsCOMVel();
457 +  double calcSysCOMVel();
458 +  double calcTotalForce();
459 +
460 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
461 +  friend class ForceSubtractionPolicy;
462 +
463   };
464  
465   #endif

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